Aleksey Portnov

Across eleven administrative districts of the Moscow region and the Moscow metropolitan area, 559 survey sites were studied from 2001 to 2020. These sites were grouped by land use types (forest, meadow and fallow land, arable land, and urban soil) and the main soil groups: Albic Podzols, Folic Retisols, Greyzemic Phaeozems, and Luvic Chernozems. At all survey sites, the dominant vegetation and geographic coordinates were recorded, and soil samples were collected from the upper 10 cm of the humus-accumulative layer. Forest soils were represented by 204 sites, meadows and fallow lands by 120, arable land by 43, soils of small towns (8 in total) by 108 sites, and those of the Moscow metropolitan area, by 84. In towns and cities, survey sites were selected in recreational, residential, and industrial land uses. The soil samples were analyzed for organic carbon (C_org), microbial biomass carbon (C_mic), basal (microbial) respiration (BR), and pH. The C_mic/C_org and BR/C_org ratios were calculated. It has been shown that the microbial parameters of soils for different land uses in small towns did not differ significantly, but in the megalopolis they did. In forest soils, the C_mic, BR, C_mic/C_org, and BR/C_org values were the highest and amounted, on average, to 589 μg C/g, 1.07 μg C–CO₂/(g h), 1.99%, and 36.0 μg C–CO₂/(g C_org h), respectively; in meadows they were lower, and in arable lands and in small towns they were the lowest (on average, 249 and 328 μg C_mic/g, 0.41 and 0.60 μg C–CO₂/(g h), 1.14 and 0.82%, 18.3 and 15.1 μg C–CO₂/(g C_org h), respectively). The spatial distribution of microbial indicators of soils in the region is visualized using the spatial interpolation method, separately for natural (forest, meadow, and fallow lands) and anthropogenically transformed (arable land, small towns) ecosystems.

Despite extensive research into green microalgae belonging to the genus Chloroidium, their species diversity and biotechnological potential remain poorly characterized. The strain VKM Al-418, the subject of this study, was isolated from the soil of Duvannyi Yar (Russian Federation). The independent species status of this strain is supported by distinct morphological characteristics, robust phylogenetic placement based on the 18S-ITS1-5.8S-ITS2 fragment, and unique features in the secondary structures of both ITS1 and ITS2, including one compensatory base change (CBC) in the highly conserved helix III of ITS2. Additionally, the species delimitation was also confirmed using five independent algorithmic approaches analyzing four different DNA barcodes. The concatenated ITS1-5.8S-ITS2 fragment is more reliable for species discrimination than the individual ITS1 or ITS2 barcodes. Of the species delimitation methods evaluated, ASAP (Assemble Species by Automatic Partitioning) and GMYC (Generalized Mixed Yule Coalescent) performed best in distinguishing Chloroidium species across multiple barcode regions in our analysis. The fatty acid profile of strain VKM Al-418 was analyzed at 9 °C, 22 °C, and 27 °C and exhibited high plasticity in response to temperature, indicative of an adaptive strategy to its harsh environment. Using this integrative taxonomic approach, we describe Chloroidium pseudoellipsoideum sp. nov., a new species with a distinct phylogenetic positioning and promising biotechnological properties.

The genus Klebsormidium is a cosmopolitan filamentous alga that belongs to the phylum Charophyta and inhabits a wide range of environments, primarily freshwater, soil, and aerial habitats. Its basal position on the Streptophyta phylogenetic tree, widespread distribution and significant functional role make the genus Klebsormidium an important object for phycological research. To advance the molecular phylogeny of Klebsormidium , we conducted the first comparative evaluation of six species delimitation methods – ASAP (Assemble Species by Automatic Partitioning), LocMin (Local Minima), KoT (K over Theta), GMYC (Generalized mixed Yule-coalescent), mlPTP (Poisson Tree Process with Maximum Likelihood), and bPTP (Poisson Tree Process with Bayesian inference) – using rbc L and concatenated ITS2– rbc L fragments. The accuracy of these methods was further validated against molecular, morphological, and ecological data. According to an integrative approach, Klebsormidium mirabile sp. nov. was proposed as a new charophyte species from soil of the Fergana Valley, Uzbekistan. In addition, a study on the fatty acid composition showed that the authentic strain VKM Al-436 of this new species of Klebsormidium is a potential source of polyunsaturated fatty acids, including linoleic, α-linolenic, and hexadecatrienoic acids.

A neural network model for individual tree detection was developed based on the YOLOv4 architecture, which underwent additional preprocessing and postprocessing steps. The preprocessing step involved expanding the dataset by randomly cutting fragments from images, calculating anchor box sizes using the K-means clustering algorithm, and discarding anchor boxes that were too small a priori. The existing post-processing block of the YOLO architecture was modified by giving more weight to false positives in the error function and using the non-maximum suppression algorithm. Baseline neural networks from the YOLOv4 and YOLOv5 architectures, each in two versions (pre-trained and not pre-trained on the MS COCO dataset), were used for comparison without any additional modifications. In the overgrown experimental field, multi-season aerial copter surveys and ground counts were conducted on several sample plots to gather data. Comparison of multi-season aerial photographs with ground-count data showed that the best images in terms of the percentage of visually identifiable trees were those taken during the snowy season and when there was no foliage. Using these images and some additional images, we manually created a dataset on which we trained and tested neural network models. The model we developed showed significantly better results (2 to 10 times better) on the mAP 0.5 metric compared to the alternatives we considered.

Despite the long research history on the genus Coelastrella, its species diversity and biotechnological potential have not been fully explored. For the first time, cluster analysis of morphological characteristics was done in the representatives of the said genus. The results obtained have shown that morphological similarity does not necessarily indicate a molecular genetic relationship. It the light of it, the taxonomic status of species can reliably be determined using specific DNA region, such as 18S–ITS1–5.8S–ITS2. The V4 and V9 regions of gene 18S rRNA are relatively conservative fragments which are not suitable for species identification. The ITS2 can be used as a “short barcode”. Among the advanced machine methods for delimitation species, the most effective algorithm for distinguishing Coelastrella species was the Generalized Mixed Yule Coalescent (GMYC) method. This paper represented for the first time our comprehensive review of the works devoted to the analysis of the biotechnological potential of representatives of the genus Coelastrella and shows that fatty acid composition of the three main chemogroups within the studied genus differs. In the future, this may form the basis for predicting the composition of the fatty acid profile of new strains, which is important while searching for organisms with specified biotechnological properties. In conclusion, an integrative approach was employed to describe Coelastrella affinis sp. nov., a new species of the genus Coelastrella with high biotechnological potential. Also, a new description of C. thermophila var. astaxanthina comb. nov. was proposed. Graphical abstract

The present study reports a new representative of Chlorella‐clade that was newly isolated from the Lake Vos'merka (Samara region, Russian Federation). 18S–ITS1–5.8S–ITS2 sequence analyses indicated that the studied strain ACSSI 368 and related Chlorella chlorelloides, Chlorella pulchelloides, formed an separate cluster in the Chlorella‐clade, unrelated to the holotype of the genus Chlorella – Chlorella vulgaris. The independent place of the genus was also confirmed by genetic distances. The individual species status of the studied strain ACSSI 368, compared with the sister C. chlorelloides, was confirmed by morphological differences (cell number per colony, type of chloroplast, number of autospores), genetic distances of the interspecific level by 18S–ITS1–5.8S–ITS2 fragment, alone by internal transcribed spacer 1 (ITS1) and internal transcribed spacer 2 (ITS2) sequences, one complementary base change in ITS1, and the results of species delimitation using five methods. A description of studied strain ACSSI 368 was provided as an authentic strain of the type species Aliichlorella ignota. Currently, the new genus Aliichlorella also includes Aliichlorella chlorelloides comb. nov. and Aliichlorella pulchelloides comb. nov. In general, six different delimitation algorithms were used in the present study. The ASAP (i.e. assemble species by automatic partitioning) and LocMin (i.e. ‘local minimum’ function) algorithms showed synchronous results, but their accuracy with respect to closely related species was somewhat lower. The mlPTP algorithm simultaneously aimed to combine closely related species in one and at the same time divide slightly distinguishing strains within a species into several molecular operational taxonomic units. The bPTP algorithm separated excessively Chlorella‐clade representatives into individual species. The generalized mixed Yule coalescent (GMYC) algorithm results were consistent the most with the modern understanding of the Chlorella‐clade taxonomy. However, the same method is one of the most time‐consuming because, for its implementation, it is necessary to carry out long preparatory work. The KoT results were less accurate than the GMYC results, although this is less time‐consuming because it does not require the preliminary construction of ultrametric trees.

We performed a quantitative and qualitative assessment of the dynamics of gap formation in the canopy of intact old-growth polydominant broadleaved forest in a permanent sample area in the Kaluga Zaseki Nature Reserve. Digital elevation models were obtained from aerial photography data of the forest in 2018 and 2021, from which gap schemas of several height classes were compiled. The resulting schemas were expertly analyzed using orthophotomosaic images, and the gap areas were estimated. A selective ground survey of gaps was carried out, and a regression analysis of the relationship between the relative gap area and the species composition of the stand based on the primary ground survey data was conducted. It was shown that the phenophase during the survey can significantly change the estimation of gap areas, and the height of the stand in the gap cannot serve as a reliable indicator of its age. It was also found that aerial photography reveals a more complex gap structure than ground-based surveys.